To import your waypoints into geoqo, just call it with the -i switch. It auto-recognizes a number of file types (.gpx being the most important).
geoqo -i myfile.gpx
If you have a .zip file from a recent pocket query, don't even bother extracting it first. geoqo can open it and pull out the contents for you:
geoqo -i myfile.zip
Your data will be stored in sets within geoqo too so you can refer to that data later. If your pocket query was named "somewhere" then you'll have a "set" of waypoints in your geoqo database named "import:somewhere" automatically for you. See the searching documentation for howto use it.
Finally, if you want to see the difference from the last time you imported a .gpx file the diff module will compare the results for you:
geoqo -i myfile.gpx+diff:out=myhtmlfile.html
Then you can open the "myhtmlfile.html" in your browser and it'll show you a nicely formatted set of changes between the previous import and you current one.